Stepping a little outside my comfort here, as I don't consider myself a good writer of romance. But I did feel the show glossed over the significance of Rory thinking Amy was talking about The Doctor. I apologize in advance if this sucks.
Amy walked into her and Rory's bunk on the TARDIS, seeing her husband already in bed, reading some medical journal. Amy smiled slightly before calling out to him.
"Rory," he looked up at the sound of her voice.
"Hey," Rory said as he shut the journal. "We all set?"
"Yeah, The Doctor is piloting our next course, although he won't tell me where he's taking us," Amy said, a hint of annoyance entering her voice as she walked over to Rory. "Rory…we need to talk."
"About what?" Rory asked as a hint of unease entered his stomach.
"Nothing bad stupid face," Amy said, trying not to laugh as she sat down next to him. "About what happened earlier."
"A lot of things happened earlier," Rory pointed out, trying to figure out where she going with this.
"About…what you thought I was saying," Amy said as she sat down next to him on the bed.
"Oh," Rory said lamely.
Amy would have laughed at the uncomfortable look on his face under any other circumstances. But after being apart for the last three months, she just wanted to be with her husband. But first, she had to make sure she knew how she really felt.
"I don't love The Doctor. I never did Rory," Amy said as she reached out, taking his hand.
"You did run away with him the night before our wedding. And you kissed him. He put a stop to that, not you," Rory pointed out lowly, not looking at her.
"I did," Amy admitted, grimacing as she recalled those actions that she'd rather forget about. "Rory…you really can't understand what it was like, growing up without parents and an aunt who didn't seem to care about me. I wish I could help you understand. For a long time, I didn't understand love. I had nothing to really compare it to. I knew you loved me, but I wasn't ready to hear it, to have it. So I settled for less. It wasn't until I lost you, that I saw you die…I love you Rory. I'm sorry it took me so long to realize it, but I do. You, not him."
"But there was a time where you did not remember me," Rory said as he finally looked at her, finally allowing himself to ask the questions that had plagued him since the day he had reunited with Amy and the Doctor. "Where you didn't know that you loved me while you were with him. Did anything ever…"
"No, never," Amy assured him quickly. "I didn't remember you but…I was sad, even though I couldn't remember why I was sad. I felt like I'd lost something very important. There was this one time that The Doctor and I helped Vincent Van Gogh - long story - and he could see how sad I was even though I didn't realize it, and I'd only known him for a few days. I couldn't remember you, but I remembered how I felt. I love you Rory Williams; you're the only man I've ever loved."
Rory was silent, processing what she said as Amy reached out her free hand, placing it on the side of his face.
"He's my best friend, and that's all he'll ever be. Was there a time I thought there might be something more? Yeah, but it was the lonely thoughts of a girl who was traumatized by nearly dying. You don't need to worry. I love you stupid face, stop being stupid," Amy said with a grin.
At this, Rory let out a chuckle and Amy knew they would be okay. If she had to spend every day assuring him that she had no feelings for The Doctor, she would. Because Rory was worth it.
"I'll never stop being stupid," Rory joked as he wrapped his arms around her, pulling her to him as Amy laughed at his antics.
I apologize in advance for any inconsistencies or anyone seemed OOC, as I'm only halfway through series six at the moment.
Hope you all enjoyed it.